Just chiming in to say, that a lot many projects now use ES6 from the start. As others have pointed out, module bundlers like Rollup, Webpack, and SystemJS have been there for quite some time, and one does not need to wait for finalisation of Module syntax, or even their implementation. If github stars were to be taken a measure of popularity / usage, then Webpack (19k) stars is pretty close to Gulp (23k) and rising faster than traditional build systems.
While it's cool if the GSAP team wants to focus on improving core animation, there hasn't been a better time to implement ES6 modules now that the bundling ecosystem has become comfortably mature and some of the many popular libraries are being re-written in ES6. There's hardly any reason to wait for browsers to implement the syntax ( a good 3-4 years before anyone starts using modules as it is). As far as maintaining separate builds are concerned, they almost never require separate maintenance, apart from a one time configuration, which gives you compatibility with UMD, ES6, and browser builds out of the box.
